Hi Ralf, Thanks for the hint. I got it to work with 'cmd /c phenix.refine' from the cygwin prompt. Was loathe to change all the .bat files as suggested in the thread, but it pointed me to the solution. Is there an overwhelming reason why .bat files are used as opposed to the old style mini .exe files? Would be really nice to have the old style back or at least the option to recreate them as a post processing step. Carsten From: [email protected] [mailto:[email protected]] On Behalf Of Ralf Grosse-Kunstleve Sent: Wednesday, January 04, 2012 11:10 PM To: PHENIX user mailing list Subject: Re: [phenixbb] CCI-Apps - Cygwin incompatibility after upgrade Hi Carsten, Could you try this? http://cygwin.com/ml/cygwin/2001-01/msg00724.html Ralf On Wed, Jan 4, 2012 at 6:28 PM, Schubert, Carsten [JRDUS] wrote: Hi, After upgrading my cci_apps install on Windows from 1.7-718 to 1.7.3-928 the interoperability with cygwin is gone. Calling phenix.refine just gives a 'Command not found' error. Turns out that the little .exe files for each subprogram were replaced by .bat files. That is fine if one just wants to use the DOS CLI, but cygwin is not able to call programs via .bat files as far as I know. Is there a workaround for this problem besides working in the DOS CLI (yuk)? Thanks Carsten _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb